Job ID = 10166099 SRX = SRX9120621 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:21 25118456 reads; of these: 25118456 (100.00%) were unpaired; of these: 808180 (3.22%) aligned 0 times 20322025 (80.90%) aligned exactly 1 time 3988251 (15.88%) aligned >1 times 96.78% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3713742 / 24310276 = 0.1528 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:40:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:40:58: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:40:58: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:04: 1000000 INFO @ Thu, 08 Oct 2020 20:41:09: 2000000 INFO @ Thu, 08 Oct 2020 20:41:15: 3000000 INFO @ Thu, 08 Oct 2020 20:41:21: 4000000 INFO @ Thu, 08 Oct 2020 20:41:26: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:41:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:41:28: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:41:28: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:32: 6000000 INFO @ Thu, 08 Oct 2020 20:41:35: 1000000 INFO @ Thu, 08 Oct 2020 20:41:39: 7000000 INFO @ Thu, 08 Oct 2020 20:41:42: 2000000 INFO @ Thu, 08 Oct 2020 20:41:46: 8000000 INFO @ Thu, 08 Oct 2020 20:41:49: 3000000 INFO @ Thu, 08 Oct 2020 20:41:53: 9000000 INFO @ Thu, 08 Oct 2020 20:41:56: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:41:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:41:58: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:41:58: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:59: 10000000 INFO @ Thu, 08 Oct 2020 20:42:02: 5000000 INFO @ Thu, 08 Oct 2020 20:42:05: 1000000 INFO @ Thu, 08 Oct 2020 20:42:06: 11000000 INFO @ Thu, 08 Oct 2020 20:42:09: 6000000 INFO @ Thu, 08 Oct 2020 20:42:12: 2000000 INFO @ Thu, 08 Oct 2020 20:42:13: 12000000 INFO @ Thu, 08 Oct 2020 20:42:16: 7000000 INFO @ Thu, 08 Oct 2020 20:42:19: 3000000 INFO @ Thu, 08 Oct 2020 20:42:19: 13000000 INFO @ Thu, 08 Oct 2020 20:42:23: 8000000 INFO @ Thu, 08 Oct 2020 20:42:25: 4000000 INFO @ Thu, 08 Oct 2020 20:42:26: 14000000 INFO @ Thu, 08 Oct 2020 20:42:29: 9000000 INFO @ Thu, 08 Oct 2020 20:42:32: 5000000 INFO @ Thu, 08 Oct 2020 20:42:33: 15000000 INFO @ Thu, 08 Oct 2020 20:42:36: 10000000 INFO @ Thu, 08 Oct 2020 20:42:39: 6000000 INFO @ Thu, 08 Oct 2020 20:42:39: 16000000 INFO @ Thu, 08 Oct 2020 20:42:43: 11000000 INFO @ Thu, 08 Oct 2020 20:42:46: 7000000 INFO @ Thu, 08 Oct 2020 20:42:46: 17000000 INFO @ Thu, 08 Oct 2020 20:42:50: 12000000 INFO @ Thu, 08 Oct 2020 20:42:52: 8000000 INFO @ Thu, 08 Oct 2020 20:42:53: 18000000 INFO @ Thu, 08 Oct 2020 20:42:56: 13000000 INFO @ Thu, 08 Oct 2020 20:42:59: 9000000 INFO @ Thu, 08 Oct 2020 20:42:59: 19000000 INFO @ Thu, 08 Oct 2020 20:43:03: 14000000 INFO @ Thu, 08 Oct 2020 20:43:05: 10000000 INFO @ Thu, 08 Oct 2020 20:43:06: 20000000 INFO @ Thu, 08 Oct 2020 20:43:10: 15000000 INFO @ Thu, 08 Oct 2020 20:43:10: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:43:10: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:43:10: #1 total tags in treatment: 20596534 INFO @ Thu, 08 Oct 2020 20:43:10: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:43:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:43:10: #1 tags after filtering in treatment: 20596534 INFO @ Thu, 08 Oct 2020 20:43:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:43:10: #1 finished! INFO @ Thu, 08 Oct 2020 20:43:10: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:43:12: #2 number of paired peaks: 176 WARNING @ Thu, 08 Oct 2020 20:43:12: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Thu, 08 Oct 2020 20:43:12: start model_add_line... INFO @ Thu, 08 Oct 2020 20:43:12: start X-correlation... INFO @ Thu, 08 Oct 2020 20:43:12: end of X-cor INFO @ Thu, 08 Oct 2020 20:43:12: #2 finished! INFO @ Thu, 08 Oct 2020 20:43:12: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:43:12: #2 alternative fragment length(s) may be 1,49,512,533,555,581 bps INFO @ Thu, 08 Oct 2020 20:43:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.05_model.r WARNING @ Thu, 08 Oct 2020 20:43:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:43:12: #2 You may need to consider one of the other alternative d(s): 1,49,512,533,555,581 WARNING @ Thu, 08 Oct 2020 20:43:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:43:12: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:43:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:43:12: 11000000 INFO @ Thu, 08 Oct 2020 20:43:16: 16000000 INFO @ Thu, 08 Oct 2020 20:43:19: 12000000 INFO @ Thu, 08 Oct 2020 20:43:23: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:43:25: 13000000 INFO @ Thu, 08 Oct 2020 20:43:29: 18000000 INFO @ Thu, 08 Oct 2020 20:43:32: 14000000 INFO @ Thu, 08 Oct 2020 20:43:36: 19000000 INFO @ Thu, 08 Oct 2020 20:43:38: 15000000 INFO @ Thu, 08 Oct 2020 20:43:42: 20000000 INFO @ Thu, 08 Oct 2020 20:43:44: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:43:45: 16000000 INFO @ Thu, 08 Oct 2020 20:43:46: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:43:46: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:43:46: #1 total tags in treatment: 20596534 INFO @ Thu, 08 Oct 2020 20:43:46: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:43:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:43:47: #1 tags after filtering in treatment: 20596534 INFO @ Thu, 08 Oct 2020 20:43:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:43:47: #1 finished! INFO @ Thu, 08 Oct 2020 20:43:47: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:43:48: #2 number of paired peaks: 176 WARNING @ Thu, 08 Oct 2020 20:43:48: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Thu, 08 Oct 2020 20:43:48: start model_add_line... INFO @ Thu, 08 Oct 2020 20:43:48: start X-correlation... INFO @ Thu, 08 Oct 2020 20:43:48: end of X-cor INFO @ Thu, 08 Oct 2020 20:43:48: #2 finished! INFO @ Thu, 08 Oct 2020 20:43:48: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:43:48: #2 alternative fragment length(s) may be 1,49,512,533,555,581 bps INFO @ Thu, 08 Oct 2020 20:43:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.10_model.r WARNING @ Thu, 08 Oct 2020 20:43:48: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:43:48: #2 You may need to consider one of the other alternative d(s): 1,49,512,533,555,581 WARNING @ Thu, 08 Oct 2020 20:43:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:43:48: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:43:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:43:51: 17000000 INFO @ Thu, 08 Oct 2020 20:43:57: 18000000 INFO @ Thu, 08 Oct 2020 20:44:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:44:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:44:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.05_summits.bed INFO @ Thu, 08 Oct 2020 20:44:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:44:03: 19000000 INFO @ Thu, 08 Oct 2020 20:44:09: 20000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:44:12: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:44:12: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:44:12: #1 total tags in treatment: 20596534 INFO @ Thu, 08 Oct 2020 20:44:12: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:44:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:44:13: #1 tags after filtering in treatment: 20596534 INFO @ Thu, 08 Oct 2020 20:44:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:44:13: #1 finished! INFO @ Thu, 08 Oct 2020 20:44:13: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:44:14: #2 number of paired peaks: 176 WARNING @ Thu, 08 Oct 2020 20:44:14: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Thu, 08 Oct 2020 20:44:14: start model_add_line... INFO @ Thu, 08 Oct 2020 20:44:14: start X-correlation... INFO @ Thu, 08 Oct 2020 20:44:14: end of X-cor INFO @ Thu, 08 Oct 2020 20:44:14: #2 finished! INFO @ Thu, 08 Oct 2020 20:44:14: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:44:14: #2 alternative fragment length(s) may be 1,49,512,533,555,581 bps INFO @ Thu, 08 Oct 2020 20:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.20_model.r WARNING @ Thu, 08 Oct 2020 20:44:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:44:14: #2 You may need to consider one of the other alternative d(s): 1,49,512,533,555,581 WARNING @ Thu, 08 Oct 2020 20:44:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:44:14: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:44:21: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:44:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:44:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:44:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.10_summits.bed INFO @ Thu, 08 Oct 2020 20:44:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:44:48: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:45:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:45:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:45:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.20_summits.bed INFO @ Thu, 08 Oct 2020 20:45:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling